3-16568941-C-G

Position:

• chr3-16568941-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.139 in 152,192 control chromosomes in the GnomAD database, including 1,878 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1878 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21210 AN: 152074 Hom.: 1874 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.125

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.139 AC: 21228 AN: 152192 Hom.: 1878 Cov.: 33 AF XY: 0.143 AC XY: 10650 AN XY: 74408

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.128

Alfa AF: 0.121 Hom.: 159

Bravo AF: 0.149

Asia WGS AF: 0.269 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4685345; hg19: chr3-16610448;